Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: A preliminary study

Li C. Xue, Rafael A. Jordan, Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)

Abstract

Computational protein-protein docking is a valuable tool for determining the conformation of complexes formed by interacting proteins. Selecting near-native conformations from the large number of possible models generated by docking software presents a significant challenge in practice. We introduce a novel method for ranking docked conformations based on the degree of overlap between the interface residues of a docked conformation formed by a pair of proteins with the set of predicted interface residues between them. Our approach relies on a method, called PS-HomPPI, for reliably predicting proteinprotein interface residues by taking into account information derived from both interacting proteins. PS-HomPPI infers the residues of a query protein that are likely to interact with a partner protein based on known interface residues of the homo-interologs of the query-partner protein pair, i.e., pairs of interacting proteins that are homologous to the query protein and partner protein. Our results on Docking Benchmark 3.0 show that the quality of the ranking of docked conformations using our method is consistently superior to that produced using ClusPro cluster-size-based and energy-based criteria for 61 out of the 64 docking complexes for which PS-HomPPI produces interface predictions. An implementation of our method for ranking docked models is freely available at: http://einstein.cs.iastate.edu/DockRank/.

Original languageEnglish (US)
Title of host publication2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011
Pages441-445
Number of pages5
DOIs
StatePublished - Dec 1 2011
Event2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011 - Chicago, IL, United States
Duration: Aug 1 2011Aug 3 2011

Publication series

Name2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011

Other

Other2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011
CountryUnited States
CityChicago, IL
Period8/1/118/3/11

Fingerprint

Proteins
Conformations
Benchmarking
Software

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

Cite this

Xue, L. C., Jordan, R. A., El-Manzalawy, Y., Dobbs, D., & Honavar, V. (2011). Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: A preliminary study. In 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011 (pp. 441-445). (2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011). https://doi.org/10.1145/2147805.2147866
Xue, Li C. ; Jordan, Rafael A. ; El-Manzalawy, Yasser ; Dobbs, Drena ; Honavar, Vasant. / Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces : A preliminary study. 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. 2011. pp. 441-445 (2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011).
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Xue, LC, Jordan, RA, El-Manzalawy, Y, Dobbs, D & Honavar, V 2011, Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: A preliminary study. in 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011, pp. 441-445, 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011, Chicago, IL, United States, 8/1/11. https://doi.org/10.1145/2147805.2147866

Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces : A preliminary study. / Xue, Li C.; Jordan, Rafael A.; El-Manzalawy, Yasser; Dobbs, Drena; Honavar, Vasant.

2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. 2011. p. 441-445 (2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Xue LC, Jordan RA, El-Manzalawy Y, Dobbs D, Honavar V. Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: A preliminary study. In 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. 2011. p. 441-445. (2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011). https://doi.org/10.1145/2147805.2147866